Knight:TOPO TA cloning - Revision history

Christopher C Vanlang: /* Patents */

2011-12-30T01:41:45Z

Patents

←Older revision		Revision as of 01:41, 30 December 2011
Line 50:		Line 50:
	#US Patent 5,827,657; Direct cloning of PCR amplified nucleic acids [[media:Herrnstadt98.pdf\|pdf]] [http://www.freepatentsonline.com/5827657.html html]		#US Patent 5,827,657; Direct cloning of PCR amplified nucleic acids [[media:Herrnstadt98.pdf\|pdf]] [http://www.freepatentsonline.com/5827657.html html]

-	[[Category:Protocol]] [[Category:In vitro]] [[Category:DNA]]	+	[[Category:Protocol]] [[Category:In vitro]] [[Category:DNA]] [[Category:cloning]]

Reshma P. Shetty at 00:19, 22 May 2007

2007-05-22T00:19:42Z

←Older revision		Revision as of 00:19, 22 May 2007
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	#US Patent 5,487,993; Direct cloning of PCR amplified nucleic acids [[media:Herrnstadt96.pdf\|pdf]] [http://www.freepatentsonline.com/5487993.html html]		#US Patent 5,487,993; Direct cloning of PCR amplified nucleic acids [[media:Herrnstadt96.pdf\|pdf]] [http://www.freepatentsonline.com/5487993.html html]
	#US Patent 5,827,657; Direct cloning of PCR amplified nucleic acids [[media:Herrnstadt98.pdf\|pdf]] [http://www.freepatentsonline.com/5827657.html html]		#US Patent 5,827,657; Direct cloning of PCR amplified nucleic acids [[media:Herrnstadt98.pdf\|pdf]] [http://www.freepatentsonline.com/5827657.html html]
		+
		+	[[Category:Protocol]] [[Category:In vitro]] [[Category:DNA]]

Reshma P. Shetty at 21:31, 5 May 2006

2006-05-05T21:31:12Z

←Older revision		Revision as of 21:31, 5 May 2006
Line 24:		Line 24:
	*In order for your part to be in BioBricks format after TOPO TA cloning, you must have the full BioBricks ends on your primers.		*In order for your part to be in BioBricks format after TOPO TA cloning, you must have the full BioBricks ends on your primers.
	*[[Austin Che]] observed anecdotally that he had a greater percentage of correct clones when he screened colonies from Kan plates rather than Amp plates.		*[[Austin Che]] observed anecdotally that he had a greater percentage of correct clones when he screened colonies from Kan plates rather than Amp plates.
		+	*Also see [[Knight:Addition of 3' A-overhangs]].

	==Resources==		==Resources==

Reshma P. Shetty: /* References */

2006-05-03T20:28:18Z

References

←Older revision		Revision as of 20:28, 3 May 2006
Line 33:		Line 33:

	==References==		==References==
		+	<biblio>
		+	#Brownstein-Biotechniques-1996 pmid=8780871
		+	#Shuman-PNAS-1991 pmid=1658796
		+	#Cheng-NAR-2000 pmid=10756188
		+	#Shuman-JBC-1994 pmid=7798275
		+	#Heyman-GenomeResearch-1999 pmid=10207160
		+	</biblio>

-	*M. J. Brownstein, J. D. Carpten, and J. R. Smith. Modulation of non-templated nucleotide addition by taq dna polymerase: primer modifications that facilitate genotyping. Biotechniques, 20(6):1004–6, 1008–10, 1996. PMID 8780871.	+	===Patents===
-	*Shuman S. Recombination mediated by vaccinia virus DNA topoisomerase I in Escherichia coli is sequence specific. Proc Natl Acad Sci U S A. 1991 Nov 15;88(22):10104-8. PMID 1658796	+	#US Patent 6,916,632; Methods and reagents for molecular cloning. (On topoisomerase-mediated cloning using a 5' overhang and blunt end.) [[media:Chesnut05.pdf\|pdf]] [http://www.freepatentsonline.com/6916632.html html]
-	*Cheng C, Shuman S. DNA strand transfer catalyzed by vaccinia topoisomerase: ligation of DNAs containing a 3' mononucleotide overhang. Nucleic Acids Res. 2000 May 1;28(9):1893-8. PMID 10756188	+	#US Patent 5,766,891; Method for molecular cloning and polynucleotide synthesis using vaccinia topoisomerase [[media:Shuman98.pdf\|pdf]] [http://www.freepatentsonline.com/5766891.html html]
-	*Shuman S. Novel approach to molecular cloning and polynucleotide synthesis using vaccinia DNA topoisomerase. J Biol Chem. 1994 Dec 23;269(51):32678-84. PMID 7798275	+	#US Patent 6,653,106; Topoisomerase based ligation and cloning methods [[media:Shuman03.pdf\|pdf]]
-	*US Patent 6,916,632; Methods and reagents for molecular cloning. (On topoisomerase-mediated cloning using a 5' overhang and blunt end.) [[media:Chesnut05.pdf\|pdf]] [http://www.freepatentsonline.com/6916632.html html]	+	#US Patent 6,548,277; Method for molecular cloning and polynucleotide synthesis using vaccinia topoisomerase [[media:Shuman03a.pdf\|pdf]] [http://www.freepatentsonline.com/6548277.html html]
-	*US Patent 5,766,891; Method for molecular cloning and polynucleotide synthesis using vaccinia topoisomerase [[media:Shuman98.pdf\|pdf]] [http://www.freepatentsonline.com/5766891.html html]	+	#US Patent 5,487,993; Direct cloning of PCR amplified nucleic acids [[media:Herrnstadt96.pdf\|pdf]] [http://www.freepatentsonline.com/5487993.html html]
-	*US Patent 6,653,106; Topoisomerase based ligation and cloning methods [[media:Shuman03.pdf\|pdf]]	+	#US Patent 5,827,657; Direct cloning of PCR amplified nucleic acids [[media:Herrnstadt98.pdf\|pdf]] [http://www.freepatentsonline.com/5827657.html html]
-	*US Patent 6,548,277; Method for molecular cloning and polynucleotide synthesis using vaccinia topoisomerase [[media:Shuman03a.pdf\|pdf]] [http://www.freepatentsonline.com/6548277.html html]	+
-	*US Patent 5,487,993; Direct cloning of PCR amplified nucleic acids [[media:Herrnstadt96.pdf\|pdf]] [http://www.freepatentsonline.com/5487993.html html]	+
-	*US Patent 5,827,657; Direct cloning of PCR amplified nucleic acids [[media:Herrnstadt98.pdf\|pdf]] [http://www.freepatentsonline.com/5827657.html html]	+
-	*J. A. Heyman, J. Cornthwaite, L. Foncerrada, J. R. Gilmore, E. Gontang, K. J. Hartman, C. L. Hernandez, R. Hood, H. M. Hull, W. Y. Lee, R. Marcil, E. J. Marsh, K. M. Mudd, M. J. Patino, T. J. Purcell, J. J. Rowland, M. L. Sindici, and J. P. Hoeffler. Genome-scale cloning and expression of individual open reading frames using topoisomerase i-mediated ligation. Genome Res, 9(1088-9051 (Print)):383–92, 1999. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=10207160 pubmed]	+

Reshma P. Shetty: /* Notes */

2006-03-16T18:38:47Z

Notes

←Older revision		Revision as of 18:38, 16 March 2006
Line 20:		Line 20:
	*Your primers should NOT have 5' phosphates. They interfere with topoisomerase I.		*Your primers should NOT have 5' phosphates. They interfere with topoisomerase I.
	*From [[Tom Knight]]: As this [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=8780871&query_hl=4 article] discusses, the 5' end of the PCR primer has a strong effect on the likelihood of 3' A addition to the PCR product when using Taq or Taq mixtures as enzymes during PCR. Since it is often necessary to add such an overhang to PCR products for cutting of an added cloning site, and since for such applications the sequence is immaterial, we should probably standardize that sequence to the A tail favoring sequence, GTTTCT for all PCR primers we make. This will favor a 3' A overhang on the PCR products, and allow TA cloning, or TOPO TA cloning of these products. Blunt end cloning could still be done by using Pfu or Phusion enzymes. I can't make any sense from the result about extending the primer sequence another base which is not specified. It seems to me this can not have any effect.		*From [[Tom Knight]]: As this [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=8780871&query_hl=4 article] discusses, the 5' end of the PCR primer has a strong effect on the likelihood of 3' A addition to the PCR product when using Taq or Taq mixtures as enzymes during PCR. Since it is often necessary to add such an overhang to PCR products for cutting of an added cloning site, and since for such applications the sequence is immaterial, we should probably standardize that sequence to the A tail favoring sequence, GTTTCT for all PCR primers we make. This will favor a 3' A overhang on the PCR products, and allow TA cloning, or TOPO TA cloning of these products. Blunt end cloning could still be done by using Pfu or Phusion enzymes. I can't make any sense from the result about extending the primer sequence another base which is not specified. It seems to me this can not have any effect.
		+	**The 3' A overhang efficiency can be promoted even further by increasing the sequence length to GTTTCTT.
	*[[Reshma Shetty]] was generating some PCR fragments via [[Annealing and primer extension \| annealing and primer extension]] and trying to [[Restriction digest \| cut with BioBricks enzymes]] and clone but the reactions were failing. Switching to TOPO TA cloning solved the problem.		*[[Reshma Shetty]] was generating some PCR fragments via [[Annealing and primer extension \| annealing and primer extension]] and trying to [[Restriction digest \| cut with BioBricks enzymes]] and clone but the reactions were failing. Switching to TOPO TA cloning solved the problem.
	*In order for your part to be in BioBricks format after TOPO TA cloning, you must have the full BioBricks ends on your primers.		*In order for your part to be in BioBricks format after TOPO TA cloning, you must have the full BioBricks ends on your primers.

Tk: /* References */

2006-01-11T04:32:23Z

References

←Older revision		Revision as of 04:32, 11 January 2006
Line 41:		Line 41:
	*US Patent 6,653,106; Topoisomerase based ligation and cloning methods [[media:Shuman03.pdf\|pdf]]		*US Patent 6,653,106; Topoisomerase based ligation and cloning methods [[media:Shuman03.pdf\|pdf]]
	*US Patent 6,548,277; Method for molecular cloning and polynucleotide synthesis using vaccinia topoisomerase [[media:Shuman03a.pdf\|pdf]] [http://www.freepatentsonline.com/6548277.html html]		*US Patent 6,548,277; Method for molecular cloning and polynucleotide synthesis using vaccinia topoisomerase [[media:Shuman03a.pdf\|pdf]] [http://www.freepatentsonline.com/6548277.html html]
-	*US Patent 5,487,993; Direct cloning of PCR amplified nucleic acids [http://www.freepatentsonline.com/5487993.html html]	+	*US Patent 5,487,993; Direct cloning of PCR amplified nucleic acids [[media:Herrnstadt96.pdf\|pdf]] [http://www.freepatentsonline.com/5487993.html html]
-	*US Patent 5,827,657; Direct cloning of PCR amplified nucleic acids [http://www.freepatentsonline.com/5827657.html html]	+	*US Patent 5,827,657; Direct cloning of PCR amplified nucleic acids [[media:Herrnstadt98.pdf\|pdf]] [http://www.freepatentsonline.com/5827657.html html]
	*J. A. Heyman, J. Cornthwaite, L. Foncerrada, J. R. Gilmore, E. Gontang, K. J. Hartman, C. L. Hernandez, R. Hood, H. M. Hull, W. Y. Lee, R. Marcil, E. J. Marsh, K. M. Mudd, M. J. Patino, T. J. Purcell, J. J. Rowland, M. L. Sindici, and J. P. Hoeffler. Genome-scale cloning and expression of individual open reading frames using topoisomerase i-mediated ligation. Genome Res, 9(1088-9051 (Print)):383–92, 1999. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=10207160 pubmed]		*J. A. Heyman, J. Cornthwaite, L. Foncerrada, J. R. Gilmore, E. Gontang, K. J. Hartman, C. L. Hernandez, R. Hood, H. M. Hull, W. Y. Lee, R. Marcil, E. J. Marsh, K. M. Mudd, M. J. Patino, T. J. Purcell, J. J. Rowland, M. L. Sindici, and J. P. Hoeffler. Genome-scale cloning and expression of individual open reading frames using topoisomerase i-mediated ligation. Genome Res, 9(1088-9051 (Print)):383–92, 1999. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=10207160 pubmed]

Reshma P. Shetty at 00:40, 11 January 2006

2006-01-11T00:40:19Z

←Older revision		Revision as of 00:40, 11 January 2006
Line 43:		Line 43:
	*US Patent 5,487,993; Direct cloning of PCR amplified nucleic acids [http://www.freepatentsonline.com/5487993.html html]		*US Patent 5,487,993; Direct cloning of PCR amplified nucleic acids [http://www.freepatentsonline.com/5487993.html html]
	*US Patent 5,827,657; Direct cloning of PCR amplified nucleic acids [http://www.freepatentsonline.com/5827657.html html]		*US Patent 5,827,657; Direct cloning of PCR amplified nucleic acids [http://www.freepatentsonline.com/5827657.html html]
		+	*J. A. Heyman, J. Cornthwaite, L. Foncerrada, J. R. Gilmore, E. Gontang, K. J. Hartman, C. L. Hernandez, R. Hood, H. M. Hull, W. Y. Lee, R. Marcil, E. J. Marsh, K. M. Mudd, M. J. Patino, T. J. Purcell, J. J. Rowland, M. L. Sindici, and J. P. Hoeffler. Genome-scale cloning and expression of individual open reading frames using topoisomerase i-mediated ligation. Genome Res, 9(1088-9051 (Print)):383–92, 1999. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=10207160 pubmed]

Reshma P. Shetty: /* References */

2006-01-10T19:23:08Z

References

←Older revision		Revision as of 19:23, 10 January 2006
Line 37:		Line 37:
	*Cheng C, Shuman S. DNA strand transfer catalyzed by vaccinia topoisomerase: ligation of DNAs containing a 3' mononucleotide overhang. Nucleic Acids Res. 2000 May 1;28(9):1893-8. PMID 10756188		*Cheng C, Shuman S. DNA strand transfer catalyzed by vaccinia topoisomerase: ligation of DNAs containing a 3' mononucleotide overhang. Nucleic Acids Res. 2000 May 1;28(9):1893-8. PMID 10756188
	*Shuman S. Novel approach to molecular cloning and polynucleotide synthesis using vaccinia DNA topoisomerase. J Biol Chem. 1994 Dec 23;269(51):32678-84. PMID 7798275		*Shuman S. Novel approach to molecular cloning and polynucleotide synthesis using vaccinia DNA topoisomerase. J Biol Chem. 1994 Dec 23;269(51):32678-84. PMID 7798275
-	*US Patent 6,916,632 on topoisomerase-mediated cloning using a 5' overhang and blunt end. [[media:Chesnut05.pdf\|pdf]] [http://www.freepatentsonline.com/6916632.html html]	+	*US Patent 6,916,632; Methods and reagents for molecular cloning. (On topoisomerase-mediated cloning using a 5' overhang and blunt end.) [[media:Chesnut05.pdf\|pdf]] [http://www.freepatentsonline.com/6916632.html html]
-	*US Patent 5,766,891, Method for molecular cloning and polynucleotide synthesis using vaccinia topoisomerase [[media:Shuman98.pdf\|pdf]]	+	*US Patent 5,766,891; Method for molecular cloning and polynucleotide synthesis using vaccinia topoisomerase [[media:Shuman98.pdf\|pdf]] [http://www.freepatentsonline.com/5766891.html html]
-	*US Patent 6,653,106, Topoisomerase based ligation and cloning methods [[media:Shuman03.pdf\|pdf]]	+	*US Patent 6,653,106; Topoisomerase based ligation and cloning methods [[media:Shuman03.pdf\|pdf]]
-	*US Patent 6,548,277; Method for molecular cloning and polynucleotide synthesis using vaccinia topoisomerase [[media:Shuman03a.pdf\|pdf]]	+	*US Patent 6,548,277; Method for molecular cloning and polynucleotide synthesis using vaccinia topoisomerase [[media:Shuman03a.pdf\|pdf]] [http://www.freepatentsonline.com/6548277.html html]
		+	*US Patent 5,487,993; Direct cloning of PCR amplified nucleic acids [http://www.freepatentsonline.com/5487993.html html]
		+	*US Patent 5,827,657; Direct cloning of PCR amplified nucleic acids [http://www.freepatentsonline.com/5827657.html html]

Tk: /* References */

2006-01-10T19:04:19Z

References

←Older revision		Revision as of 19:04, 10 January 2006
Line 38:		Line 38:
	*Shuman S. Novel approach to molecular cloning and polynucleotide synthesis using vaccinia DNA topoisomerase. J Biol Chem. 1994 Dec 23;269(51):32678-84. PMID 7798275		*Shuman S. Novel approach to molecular cloning and polynucleotide synthesis using vaccinia DNA topoisomerase. J Biol Chem. 1994 Dec 23;269(51):32678-84. PMID 7798275
	*US Patent 6,916,632 on topoisomerase-mediated cloning using a 5' overhang and blunt end. [[media:Chesnut05.pdf\|pdf]] [http://www.freepatentsonline.com/6916632.html html]		*US Patent 6,916,632 on topoisomerase-mediated cloning using a 5' overhang and blunt end. [[media:Chesnut05.pdf\|pdf]] [http://www.freepatentsonline.com/6916632.html html]
		+	*US Patent 5,766,891, Method for molecular cloning and polynucleotide synthesis using vaccinia topoisomerase [[media:Shuman98.pdf\|pdf]]
		+	*US Patent 6,653,106, Topoisomerase based ligation and cloning methods [[media:Shuman03.pdf\|pdf]]
		+	*US Patent 6,548,277; Method for molecular cloning and polynucleotide synthesis using vaccinia topoisomerase [[media:Shuman03a.pdf\|pdf]]

Reshma P. Shetty: /* References */

2006-01-10T18:50:18Z

References

←Older revision		Revision as of 18:50, 10 January 2006
Line 37:		Line 37:
	*Cheng C, Shuman S. DNA strand transfer catalyzed by vaccinia topoisomerase: ligation of DNAs containing a 3' mononucleotide overhang. Nucleic Acids Res. 2000 May 1;28(9):1893-8. PMID 10756188		*Cheng C, Shuman S. DNA strand transfer catalyzed by vaccinia topoisomerase: ligation of DNAs containing a 3' mononucleotide overhang. Nucleic Acids Res. 2000 May 1;28(9):1893-8. PMID 10756188
	*Shuman S. Novel approach to molecular cloning and polynucleotide synthesis using vaccinia DNA topoisomerase. J Biol Chem. 1994 Dec 23;269(51):32678-84. PMID 7798275		*Shuman S. Novel approach to molecular cloning and polynucleotide synthesis using vaccinia DNA topoisomerase. J Biol Chem. 1994 Dec 23;269(51):32678-84. PMID 7798275
-	*US Patent 6,916,632 on ~~Topo~~-TA cloning [[media:Chesnut05.pdf\|pdf]] [http://www.freepatentsonline.com/6916632.html html]	+	*US Patent 6,916,632 on topoisomerase-mediated cloning using a 5' overhang and blunt end. [[media:Chesnut05.pdf\|pdf]] [http://www.freepatentsonline.com/6916632.html html]